The expression data were obtained via the Gene Expression Omnibus and StemBase, or were kindly supplied by the authors. Microarray probes were mapped to the mouse ENSEMBL
gene database (NCBI m37 assembly) and discretised to present (P), absent
(A), or unknown (U) values (if the gene was not represented on the
array). To do this, all 271 distinct arrays were processed with
the mas5calls method of the affy library.
In order to diminish the number of false positives, all probe sets with
p-values >0.04 were annotated as 'A' (absent). For those
studies that included biological replicates, the following strategy was
adopted: if the p-values of a given probe were <=0.04 in >50% of
biological replicates, then the probe in question was flagged as 'P' in
that particular cell type. Most genes on the Affymetrix arrays
present in the database are represented by a single probe. As a
second step for those genes represented by multiple probes, then only
if >50% of probes were labelled as 'P' from the previous step, then
the gene was recorded as 'P'.